rigid body not rotating after collision
What is preventing you from applying scale is that more than one object in your scene shares the same mesh.  This object was instanced instead of duplicated.

The solution should be to right click on one of the offending meshes in the Outliner and select Make Single User, but this is evidently not yet implemented.
Instead, what may be easiest is to duplicate each object in place with Shift+D, cancel movement with RMB and delete the originals.
When each object has unique mesh data, you'll be able to apply scale to all of them.